Multiple sequence alignment - TraesCS1A01G233000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G233000 chr1A 100.000 2642 0 0 1 2642 406218768 406216127 0.000000e+00 4879
1 TraesCS1A01G233000 chr5A 94.102 2645 151 5 1 2642 480421659 480424301 0.000000e+00 4015
2 TraesCS1A01G233000 chr4D 92.066 2647 198 8 1 2642 34624588 34621949 0.000000e+00 3714
3 TraesCS1A01G233000 chr7A 78.366 453 90 8 89 537 653420156 653420604 1.200000e-73 287


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G233000 chr1A 406216127 406218768 2641 True 4879 4879 100.000 1 2642 1 chr1A.!!$R1 2641
1 TraesCS1A01G233000 chr5A 480421659 480424301 2642 False 4015 4015 94.102 1 2642 1 chr5A.!!$F1 2641
2 TraesCS1A01G233000 chr4D 34621949 34624588 2639 True 3714 3714 92.066 1 2642 1 chr4D.!!$R1 2641

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
483 484 1.512926 GATGCACAAGTTCGTGAGGT 58.487 50.0 8.92 0.0 39.34 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2363 0.179137 TGCTCACCGTATCAGCTTCG 60.179 55.0 0.0 0.0 34.03 3.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.911651 TGGTAGGGCAATTTTCATTTTTCATA 58.088 30.769 0.00 0.00 0.00 2.15
33 34 8.667463 AGGGCAATTTTCATTTTTCATATTTCG 58.333 29.630 0.00 0.00 0.00 3.46
48 49 9.632807 TTTCATATTTCGTTTTGGGTTCATTAG 57.367 29.630 0.00 0.00 0.00 1.73
69 70 3.809832 AGTGCCATCAATTATACTCACGC 59.190 43.478 0.00 0.00 0.00 5.34
134 135 6.324254 AGGTCGCTATTAAGAATGTACTTCCT 59.676 38.462 0.00 0.00 34.11 3.36
142 143 3.858247 AGAATGTACTTCCTAACACGGC 58.142 45.455 0.00 0.00 34.11 5.68
286 287 1.528129 GAGTTTGAGGAGGCTTGGTG 58.472 55.000 0.00 0.00 0.00 4.17
366 367 5.082425 AGATCAGAGAAAAATGGGCAAAGT 58.918 37.500 0.00 0.00 0.00 2.66
383 384 2.814280 AGTCGTACTTCAAGGGTGTG 57.186 50.000 0.00 0.00 0.00 3.82
446 447 3.738282 CGAACCATATGCTGAAGAGCTAC 59.262 47.826 0.00 0.00 46.39 3.58
483 484 1.512926 GATGCACAAGTTCGTGAGGT 58.487 50.000 8.92 0.00 39.34 3.85
576 577 3.085952 AGCTGGTAAATAGGCAAGCAA 57.914 42.857 0.00 0.00 33.08 3.91
578 579 4.026052 AGCTGGTAAATAGGCAAGCAAAT 58.974 39.130 0.00 0.00 33.08 2.32
579 580 4.114794 GCTGGTAAATAGGCAAGCAAATG 58.885 43.478 0.00 0.00 0.00 2.32
747 751 3.391626 TGGAGGCTATCGAGTAGAAGAGA 59.608 47.826 0.00 0.00 31.71 3.10
818 822 3.352648 AGAGAAGTGGAGCAGAGTAGTC 58.647 50.000 0.00 0.00 0.00 2.59
919 923 5.431765 CTGCCATGTTCTGAAGGTAGTAAT 58.568 41.667 4.72 0.00 0.00 1.89
924 928 6.316390 CCATGTTCTGAAGGTAGTAATGGAAC 59.684 42.308 0.00 0.00 35.16 3.62
940 944 2.675844 TGGAACACTGGATTTAATCGCG 59.324 45.455 0.00 0.00 0.00 5.87
972 976 5.177511 TCGCTGATAACTGCATATTAAGTGC 59.822 40.000 8.30 8.30 42.81 4.40
981 985 5.068198 ACTGCATATTAAGTGCCAATTCCTG 59.932 40.000 11.71 0.00 41.83 3.86
1020 1024 2.335681 TGGACTACTTGGGGATGACA 57.664 50.000 0.00 0.00 0.00 3.58
1152 1156 2.779755 TCAGGCACAACCGAATGTAT 57.220 45.000 0.00 0.00 46.52 2.29
1240 1244 1.610038 TGTTCAAGCAAGCCATGACTG 59.390 47.619 0.00 0.00 0.00 3.51
1242 1246 1.985473 TCAAGCAAGCCATGACTGTT 58.015 45.000 0.00 0.00 0.00 3.16
1259 1263 1.205179 TGTTATGGCACCGTACGACAT 59.795 47.619 18.76 16.49 0.00 3.06
1270 1274 0.530744 GTACGACATGCAGAGGGACA 59.469 55.000 0.00 0.00 0.00 4.02
1416 1420 2.843113 AGCTAAGAAGAGGAATGCAGGT 59.157 45.455 0.00 0.00 0.00 4.00
1441 1445 1.661341 CACCAATGCTAGAGACAGGC 58.339 55.000 0.00 0.00 0.00 4.85
1529 1533 1.153647 CTACATGCCCGCAACGAGA 60.154 57.895 0.00 0.00 0.00 4.04
1572 1576 3.950395 GGAAAGAAGGTAGATGCAGCAAT 59.050 43.478 4.07 0.00 0.00 3.56
1614 1618 1.365699 AAAACACGTGCGACAGAGTT 58.634 45.000 17.22 0.00 0.00 3.01
1767 1771 3.572255 GCTGTCCCAATAAGGTGTTTGAA 59.428 43.478 0.00 0.00 34.66 2.69
1814 1819 2.736081 CGCGGTGTAGCTACATTTACCA 60.736 50.000 28.37 1.63 38.63 3.25
1825 1830 6.769512 AGCTACATTTACCATCCGATATGTT 58.230 36.000 0.00 0.00 0.00 2.71
1849 1854 1.393539 CCCAGAGAAAATACACGTGCG 59.606 52.381 17.22 0.00 0.00 5.34
1970 1975 3.379865 TTAGTGCGGGCGGGATGTC 62.380 63.158 0.00 0.00 0.00 3.06
1989 1994 2.102084 GTCCCACCCGGAGTTAGTATTC 59.898 54.545 0.73 0.00 43.19 1.75
2059 2066 3.233980 TGAGTGCCGCTCCAGTGT 61.234 61.111 2.25 0.00 43.48 3.55
2167 2174 1.113788 CGCCCCCAACATTCATCAAT 58.886 50.000 0.00 0.00 0.00 2.57
2187 2194 6.446318 TCAATGATGAGGTTAGTGCAAAAAC 58.554 36.000 0.00 0.00 0.00 2.43
2215 2222 2.561569 GCTGCTATGTTTCCGTGGTAT 58.438 47.619 0.00 0.00 0.00 2.73
2350 2357 2.927856 TCGGAAGCAGGGCAAGGA 60.928 61.111 0.00 0.00 0.00 3.36
2356 2363 0.752658 AAGCAGGGCAAGGAAACAAC 59.247 50.000 0.00 0.00 0.00 3.32
2460 2467 4.211125 TGGTTTGTTGTTGCAGGAATCTA 58.789 39.130 0.00 0.00 0.00 1.98
2470 2477 1.879796 GCAGGAATCTATGGAAGGCCG 60.880 57.143 0.00 0.00 36.79 6.13
2505 2512 2.367377 AGGCTGGCATCTGGGCTA 60.367 61.111 3.38 0.00 43.83 3.93
2595 2602 2.611224 CCAAAAGATTTGGAGGCAGTGC 60.611 50.000 15.17 6.55 42.06 4.40
2617 2624 2.232452 CCGAAGAAGACAGTGTGGATCT 59.768 50.000 0.00 0.00 0.00 2.75
2624 2631 1.002430 GACAGTGTGGATCTGCTGGAA 59.998 52.381 0.00 0.00 36.50 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.227152 GCACTAATGAACCCAAAACGAAAT 58.773 37.500 0.00 0.00 0.00 2.17
33 34 4.021544 TGATGGCACTAATGAACCCAAAAC 60.022 41.667 0.00 0.00 0.00 2.43
36 37 3.448093 TGATGGCACTAATGAACCCAA 57.552 42.857 0.00 0.00 0.00 4.12
40 41 9.056005 TGAGTATAATTGATGGCACTAATGAAC 57.944 33.333 0.00 0.00 0.00 3.18
48 49 3.362986 CGCGTGAGTATAATTGATGGCAC 60.363 47.826 0.00 0.00 0.00 5.01
69 70 0.729140 GCATTTTTGACCCGCTCACG 60.729 55.000 0.00 0.00 39.67 4.35
76 77 3.841643 CACTGATCTGCATTTTTGACCC 58.158 45.455 0.00 0.00 0.00 4.46
134 135 2.811747 CACCGATGCGCCGTGTTA 60.812 61.111 4.18 0.00 0.00 2.41
142 143 1.358725 CCACTTACACCACCGATGCG 61.359 60.000 0.00 0.00 0.00 4.73
366 367 2.696707 AGAACACACCCTTGAAGTACGA 59.303 45.455 0.00 0.00 0.00 3.43
383 384 1.014044 TCGTCATCTTGGCGCAGAAC 61.014 55.000 10.83 0.00 46.34 3.01
416 417 0.855349 GCATATGGTTCGCACTCTCG 59.145 55.000 4.56 0.00 0.00 4.04
483 484 5.414454 GGTCAAACTGCAACCTCATGTATTA 59.586 40.000 0.00 0.00 0.00 0.98
594 598 4.876107 CCACGGAATGCTTCAGTTATTAGT 59.124 41.667 0.00 0.00 35.91 2.24
714 718 0.323999 TAGCCTCCAGCCTCGTACAA 60.324 55.000 0.00 0.00 45.47 2.41
818 822 4.100529 CGCTTAGCATTTTCACCATGAAG 58.899 43.478 4.70 0.00 37.70 3.02
869 873 0.821301 TGCCCATGTGCTCGAACAAA 60.821 50.000 0.86 0.00 32.81 2.83
891 895 1.610038 CTTCAGAACATGGCAGCACAA 59.390 47.619 0.00 0.00 0.00 3.33
919 923 2.675844 CGCGATTAAATCCAGTGTTCCA 59.324 45.455 0.00 0.00 0.00 3.53
924 928 1.013596 TGCCGCGATTAAATCCAGTG 58.986 50.000 8.23 0.00 0.00 3.66
929 933 0.928229 AGACGTGCCGCGATTAAATC 59.072 50.000 8.23 0.00 44.77 2.17
940 944 0.179134 AGTTATCAGCGAGACGTGCC 60.179 55.000 0.00 0.00 0.00 5.01
945 949 6.642950 ACTTAATATGCAGTTATCAGCGAGAC 59.357 38.462 0.00 0.00 0.00 3.36
972 976 2.481185 GCATGCAAAACACAGGAATTGG 59.519 45.455 14.21 0.00 0.00 3.16
981 985 0.388659 TCACCTGGCATGCAAAACAC 59.611 50.000 21.36 0.64 0.00 3.32
1020 1024 8.006298 TGACTATGTGTTTCTTTGGAATTGTT 57.994 30.769 0.00 0.00 0.00 2.83
1080 1084 1.004560 GTAGTGCTGCAGGTGCTCA 60.005 57.895 17.12 0.71 42.66 4.26
1170 1174 1.077429 GGCATCTCCCAACCTGACC 60.077 63.158 0.00 0.00 0.00 4.02
1240 1244 1.591158 CATGTCGTACGGTGCCATAAC 59.409 52.381 16.52 3.92 0.00 1.89
1242 1246 0.528901 GCATGTCGTACGGTGCCATA 60.529 55.000 22.06 2.15 0.00 2.74
1259 1263 3.324930 CCAGCCTGTCCCTCTGCA 61.325 66.667 0.00 0.00 0.00 4.41
1349 1353 3.818180 CTCCCCTCATCTTGATTCTTGG 58.182 50.000 0.00 0.00 0.00 3.61
1416 1420 1.971505 CTCTAGCATTGGTGGGGCGA 61.972 60.000 0.00 0.00 0.00 5.54
1441 1445 1.810412 GCTAAGCCCTTCGTATGGTGG 60.810 57.143 0.00 0.00 0.00 4.61
1572 1576 1.769716 TATGTCCCGCCACACCACAA 61.770 55.000 0.00 0.00 0.00 3.33
1639 1643 7.265673 AGAAAAATTCAGCTATCGCACTACTA 58.734 34.615 0.00 0.00 39.10 1.82
1650 1654 8.812972 TCTACAGTTAGGAGAAAAATTCAGCTA 58.187 33.333 0.00 0.00 0.00 3.32
1651 1655 7.680730 TCTACAGTTAGGAGAAAAATTCAGCT 58.319 34.615 0.00 0.00 0.00 4.24
1767 1771 6.827586 TCGCCTTATATCAAACCAAACTTT 57.172 33.333 0.00 0.00 0.00 2.66
1797 1801 4.940463 TCGGATGGTAAATGTAGCTACAC 58.060 43.478 28.28 15.35 39.30 2.90
1814 1819 3.967326 TCTCTGGGACAAACATATCGGAT 59.033 43.478 0.00 0.00 38.70 4.18
1825 1830 4.062293 CACGTGTATTTTCTCTGGGACAA 58.938 43.478 7.58 0.00 38.70 3.18
1849 1854 5.474578 TTCTCAGGACATCCATACTATGC 57.525 43.478 0.00 0.00 38.89 3.14
1953 1958 3.845259 GACATCCCGCCCGCACTA 61.845 66.667 0.00 0.00 0.00 2.74
1970 1975 2.112998 TGAATACTAACTCCGGGTGGG 58.887 52.381 0.00 0.00 35.24 4.61
2059 2066 7.384115 GCTTGATCTACTACTAACAACACAACA 59.616 37.037 0.00 0.00 0.00 3.33
2158 2165 6.124340 TGCACTAACCTCATCATTGATGAAT 58.876 36.000 25.29 17.83 46.51 2.57
2167 2174 3.572255 GGGTTTTTGCACTAACCTCATCA 59.428 43.478 22.04 0.00 42.72 3.07
2187 2194 0.392998 AAACATAGCAGCGACCTGGG 60.393 55.000 0.00 0.00 39.54 4.45
2222 2229 1.650242 TTCCTTCAGCCACCACCCAA 61.650 55.000 0.00 0.00 0.00 4.12
2264 2271 0.313987 TCGCTCTCAGACGCTTCAAA 59.686 50.000 0.00 0.00 0.00 2.69
2337 2344 0.752658 GTTGTTTCCTTGCCCTGCTT 59.247 50.000 0.00 0.00 0.00 3.91
2350 2357 2.478894 CACCGTATCAGCTTCGTTGTTT 59.521 45.455 0.00 0.00 0.00 2.83
2356 2363 0.179137 TGCTCACCGTATCAGCTTCG 60.179 55.000 0.00 0.00 34.03 3.79
2460 2467 3.560251 CCCGATCCGGCCTTCCAT 61.560 66.667 0.00 0.00 46.86 3.41
2470 2477 1.337260 CCTCGTCATTCATCCCGATCC 60.337 57.143 0.00 0.00 0.00 3.36
2483 2490 2.580815 CAGATGCCAGCCTCGTCA 59.419 61.111 0.00 0.00 0.00 4.35
2505 2512 3.069872 TCTGCACCATTTGTTTCAGCATT 59.930 39.130 0.00 0.00 0.00 3.56
2542 2549 1.676967 CCACCTTCTTGCAGCTCCC 60.677 63.158 0.00 0.00 0.00 4.30
2577 2584 1.260544 GGCACTGCCTCCAAATCTTT 58.739 50.000 13.28 0.00 46.69 2.52
2595 2602 0.679505 TCCACACTGTCTTCTTCGGG 59.320 55.000 0.00 0.00 0.00 5.14
2596 2603 2.232452 AGATCCACACTGTCTTCTTCGG 59.768 50.000 0.00 0.00 0.00 4.30
2603 2610 0.612229 CCAGCAGATCCACACTGTCT 59.388 55.000 0.00 0.00 37.64 3.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.